Modify animated Armature BGE
The action actuator will play the animation of the action. This animation consists of several channels. On armature actions these channels are the channels of the single bones. Typical channels are location, rotation, scale.
When the animation plays a channel it sets the pose of the bone regardless what pose the bone had before.
When you want to pose the channel via Python you should ensure this channel is not set within the action otherwise it gets overridden (the animation gets applied after the Python controller set the pose).
Solution
Remove all channels you want to manipulate via Python from within the action

Hint
When you play two actions that share the same channel only one of the actions will be played (unless